Microwaves do extra damage to shields, while they're not intended as anti-shield weapons, this does help to break through shields so they can be effective, what about a similar mechanic for mesons?
Thick armour negates most hits of mesons, but perhaps they could do enhanced damage to armour while still doing single points against internals? Maybe affected by calibre, higher calibre doing 2 or 3 damage to armour, making mesons a superiour sandpapering weapon, or perhaps just higher calibre helping to penetrate more armour layers, lower chance of hitting each layer of armour?